Entering edit mode
3.2 years ago
Dominik_H
•
0
Hello, i was trying to use ASpli package to analyze alternative splicing events in my RNA-Seq data in R. As input i used human hg38 gtf from ucsc and .bam files produced by BWA.
TxDb <- makeTxDbFromGFF(file="hg38.ncbiRefSeq.gtf",format="gtf")
features <- binGenome(TxDb)
BAMFiles <- c("bam1.bam", "bam2.bam", "bam3.bam", "bam4.bam")
targets <- data.frame(bam = BAMFiles, genotype = c( "phenotype1", "phenotype1", "phenotype2", "phenotype2"), stringsAsFactors = FALSE )
gbcounts <- gbCounts( features = features,targets = targets,minReadLength = 30, maxISize = 50000,libType="PE",strandMode=0)
I got an error:
*Error in matrix("", n, max(nc)) : invalid 'ncol' value (too large or NA)
In addition: There were 34 warnings (use warnings() to see them)*
If anyone has an idea what could be an issue, i am greatfull for any suggestion. I tried using different gtfs and chromosomes dont have different naming. Thank you.
